Dark Skyeward
by Gleek-Whovianfangirl
Summary: Name will be changed, when I can think of a better one. Rated T for violence and darker themes later on in this story. All of Team Bus involved. (I'm bad at summaries, sorry) What if Ward wasn't the only traitor on the plane, what if he had a partner in crime? - Skye nodded and came and sat beside him. "Good. I don't like sharing you." She said with a small smile
1. Chapter 1

**So I read a fanfic, which I can't remember the name of but if anyone wants it I'm sure I can dig a little to find it, and this is basically what came to mind when I thought about the possibility of both Ward and Skye being Hydra.**

* * *

"You slept with Lorelei?" She asked, her arms folded against her chest while stood in the centre of his bunk. Simmons had allowed her to walk around the Bus as long as she was cautious and told her of anything that could be dangerous to her.

"It's not like it was out of choice. Do you really think I'd willingly fall into bed with anyone like that?" He asked with a frown as he shifted the ice pack at the side of his face, he forgot how hard May's punches were and a large purple bruise was already blossoming on the side of his face.

"Well you did it with May too." She mumbled and looked down, her shoes were suddenly a lot more interesting than before.

"I could say the same about you and your ex then." He told her and groaned as the ice pack rested on the cut that had also been caused from falling through the glass, something that wasn't intentional.

"That was for the mission and you know it."

"So was me and May. Just, you know, not the same mission." He shrugged.

Skye looked up again at those words. "What happened? You didn't blow our cover did you?"

"Do you really think if I blew our covers we'd be having this conversation here of all places." He asked. "I told the Asgardian who I desired apparently, she figured out it wasn't her and told me I had to be honest with myself or whatever. She ended it."

Skye nodded and came and sat beside him. "Good. I don't like sharing you." She said with a small smile and she placed her hand on his uninjured cheek. "I still hate that the only way to get her to trust you was to repeatedly end up in bed with her, but it's all done now." She smiled and leaned in, pecking him on the lips gently. They'd kissed in private when no one was with them which mostly meant at ridiculous hours in the morning so it could be kept a secret and they'd slept with each other since they'd arrived on the bus but she missed how they couldn't hold hands in public and she missed the feeling of waking up to their legs tangled together.

"We still can't do this around the others. I'm a by the books agent. It's against protocol." He said with a half smile. He wished he could completely ignore everything he'd been taught but he couldn't. His boss wouldn't be impressed with that considering he was one of their best agents, along with Skye, who played a clueless, not even agent, brilliantly. "But what they don't know won't hurt them." He whispered and dropped the ice pack beside him so he could hold her face with both his hands and kiss her, rougher than he had intended to but she was showing no signs of wanting him to stop.

"This doesn't look like taking it easy, either of you." Came a British voice, Simmons. Skye jumped away with a blush and quickly brushed her hair down with her fingers, it had become disheveled from Ward's hands. She knew he loved it and could hear the low groan from him before he pulled his gaze away from her.

"So this isn't what it looks like..." Started Skye.

"Yeah..heat of the moment thing." Ward continued before grabbing the ice pack and holding it back to his face after he saw Simmons glaring at the pack like it would just magically appear on his cheek again. She looked redder than Skye did at having caught them.

"I just came to check Skye was okay, but apparently she seems fine so I'll be on my way." She told them, avoiding eye contact before walking off. Skye and Ward could hear her muttering the words 'Fitz owes me 30 bucks' as she left.

"That's what I imagine my mum walking in on me would feel like. I feel like a tennager." Skye said with a giggle that he loved.

"Don't get used to it, it can't happen again. I fear I'll get killed by Coulson before anything else can happen." He said and stood up, offering his right hand to help her up too, knowing she still had a little trouble with movement from the shooting, which he would be bringing up with Quinn later on. Skye took his hand and with the help of him stood up, placing a quick kiss on his lips.

"That was the last one for now, I promise." She grinned and released his hand before pushing her hair from her face. "Judging by the bruise on your face I'm surprised she didn't knock you out, it looks more like face paint than a bruise. An unnatural purple." She teased with a wink before walking off, leaving him stood in the centre of the room.

* * *

Skye made the mistake of going down to the lab for more pain meds. As usual FitzSimmons were doing what they usually do but stopped as soon as she entered the room, a smug grin on Simmons while Fitz was just smiling. "You want to explain what I saw now I've recovered?" Simmons asked and leaned across the work bench to see her better without the larger than normal microscope blocking her view of the young hacker.

"Not really. I need some more meds, it's been hours since my last ones and I'm starting to feel something that I probably shouldn't."

"Ward probably helped with that." Fitz cut in with the same smug grin as Simmons had on her.

"If Ward made me feel pain where I've been shot I'm sure we'd have a problem wouldn't we." She told him sarcastically. "We kissed, probably due to adrenaline from today. Nothing more, nothing less, nothing's changed other than the fact you've lost some money to your partner." She continued and nodded a thank you as two more pills got placed in her outstretched palm. She quickly swallowed them and downed the small cup of water Simmons had handed to her.

"So you heard about that then?" The bio-chemist asked with a slight grimace.

"Of course we did. You're as good at being quiet as you are lying." She told her before May walked in. She shot a warning look between the two usual occupants of the lab as a warning of not to tell her what had been seen only minutes ago. Skye looked back at May, who looked rougher than usual, she was still a little bloodied from earlier and her hand looked swollen but she also looked annoyed at everything in her eyeline, especially Skye. Maybe she did have feelings for Ward, not that she felt bad at all for playing a part in those two ending what was going on.

"So how much damage was done to the Bus in the end? I heard you were running diagnostics to find out." Skye said, trying to ease the tension they all felt in the room.

"Fury won't be as pissed as he was the last time as the exterior's still in tact and inside it was nothing major, just glass, couches etc. Ward already said he'd clean it up so I'm not worried." May shrugged and didn't make any eye contact with Skye. "I'm sure he'd love it if you helped him." FitzSimmons chuckled at May and she frowned. "I missed something didn't I?"

"Only the fact the pair locked lips." Said the Scotsman.

"What are you! Twelve?" Skye asked and threw her hands up to accentuate her point. "Who even says that now or is it a Scottish thing." She asked with a frown and placed her hands on her hips and made the quick decision to leave without another word, knowing she'd only end up diggingn herself deeper.

"Are you okay Agent May?" Simmons asked. "You just seem quite angry and I can't think of a time when that was ever good." She explained quietly, scared May would lash out at her. She really didn't want that. "I can help you clean your hand up if you want." She said and stepped closer as the older agent grabbed some antiseptic wipes and a bandage.

"It's fine. I've had worse." She said bluntly before she disappeared up to the cockpit.

"She didn't seem very fine did she?" She asked and turned to Fitz who just shrugged.

* * *

"I heard you aren't in the best of moods today." Coulson said, in his usual upbeat tone that usually made everyone smile, from the co-pilots seat. She jumped not expecting him to be sat there but quickly recovered and sat beside him.

"Some psycho alien invaded our plane, after possessing two agent which lead to two of us getting beat up. Why would I be in a good mood?" She asked and cleaned the cuts on her hand gently, not even wincing.

"So is everything still okay with you and Ward after what we know happened at the hotel?"

Melinda tensed up knowing that question would come up. "There is no me and Ward. He has a thing for Skye so I ended it, didn't bother him apparently." She muttered and tied the bandage around her hand tighter than necessary.

He didn't catch the end of what she was saying as she began to trail of, obviously not wanting to be heard. "Good." She looked up with a frown about to reply but he continued. "I don't mean good about the whole Ward going after Skye thing." He clarified and turned to look at her. "I feel like something's going on behind our backs but I can't quite put my finger on it, I don't even know if it's actually going on, I'm just suspecting something is." He told her. "I'll come back when I have more. Just take care of yourself okay?" He asked before getting up to leave but not without rubbing her shoulder gently.

* * *

"I didn't think you were the cleaning type?" Skye asked as she sat herself down on the now correctly positioned couch beside him as he sweeped up glass shards from the carpet. She'd figured it best she not bend down to his level due to her injuries.

"I'm not, but seeing as I'm partly responsible, I decided I probably should do my bit." He shrugged and bought the plastic bag full of glass closer to him before emptying the pan into it.

"I could get used to seeing you all domestic. It suits you." She teased and kicked his shoulder gently but enough to make him sway a little, to her amusement.

"I don't plan on getting thrown through any glass windows anytime soon, so it's probably best you don't get used to it." He said with a smile as he looked up at her. "Have you contacted him yet? We need to check in soon." He asked. They refrained from using his name in case any of their fellow Shield agents walked past while they spoke about it, with no name they could just pass it off as a friend as neither of them were in contact with most of their family, Gramsy being the exception.

"I was going to wait for you before I do it, you probably know a little more than me seeing as I've been pretty much isolated for over two weeks." She told him and watched as he stood up, looking as handsome as ever in his tight white shirt and messy hair.

"Then I'm ready when you are, I'll go over all of this with a vacuum a little later, he'll get mad if we keep him waiting too long. You know how he is."

"Considering he killed the last agent who didn't check in, even though he was being held hostage, I think we both know how he is." Skye said, with a shudder, she couldn't hate the man after all he'd done for the pair of them, but sometime his lack of remorse frightened her to the point of her wishing she didn't work for him.

They both walked towards Ward's room and he activated a small device, once the door was shut, which soundproofed the room they were in, it was a going away gift as they started at Shield. Skye dialed the number once she saw the device light up green, a sign that it was in us, his number was under the name 'Susan' to prevent anyone getting nosey if they went on her phone. It rung four times before she answered with her usual opening sentence.

"We only have a few minutes."

"Then get talking, princess." Replied the rough voice.

* * *

 **A/N I hoped you enjoyed the first chapter! I don't know how many chapter's this will be (If people like it) but I know what I want to happen in it, got it all written down. But this is the most I've ever written for one chapter on here.**

 **Any mistakes are my own, I don't have a beta.**

 **So if you liked please follow, favourite and review, it'll motive me to write updates quicker, reviews do that quicker ;)**


	2. Chapter 2

**I'm overwhelmed with the response for the first chapter, so thank you to all those who reviewed, favourited and followed.**

 **Special thanks to those who reviewed - Alkeni, NN010, Sparkygirl123, 8abbie8, Silverslitherer, everyfandom1, Annavale23, Misha and the 3 Guests. Your reviews made my day.**

 **Special thanks to Sparkygirl123 who is now beta'ing this fanfic so you won't have to put up with any of my mistakes!**

* * *

 _"Then get talking, princess." Replied a rough voice._

Before Skye could even open her mouth to start filling him in on what was happening Ward took the phone from her open palm. "Before we go into details, I wanted to know why you thought Quinn shooting Skye was ever a good idea. We're two weeks behind on what we intended to do now and on top of that she has alien DNA injected into her body." Ward said, his tone angry.

"I know. I was there." Was the blunt reply. "It's what needed to happen. I won't say I'm sorry for it because now we have what we needed. We have the GH-325, even if it's not how we intended we can draw blood and see what it does." Skye looked up at Ward, she knew Simmons was pretty much trying to do the same thing and was failing, and it was bad if she couldn't do it.

"Sir, one of the scientists is already trying to do what you want to do, she claims if she can manage to do it it can be distributed throughout all of SHIELD, save the lives of the unsaveable. What do we do about that? She's being taking the blood while Skye was was out and I didn't know."

There was silence on the phone for a moment.

"Take her out."

"Are you joking? If we take her out our cover will be blown way to soon. We won't accomplish everything you needed done, our purpose of staying undercover will be pointless!" Skye told him angrily.

Grant gave her a stern look, telling her non-verbally not to raise her voice at him. He knew first hand what he was capable of when he got angry at the pair and Ward was always willing to take the punches and kicks for her.

There was silence at the other end of the line for what felt like hours.

"I'm giving you a choice here. You take her out or find a way to grab all of her findings without getting caught. You're right, it's too early but it might need to happen if the circumstances are bad. I need Skye back here, alive, one way or another to get the serum from her. I have to go, stay safe kids!" He said before the line went dead. Ward shoved the phone under his bed and took the small device that soundproofed the room before looking up at his partner who was frowning at him.

"What?" He asked.

"He doesn't care if you get out of here alive." She frowned. "Does that not concern you? The way he phrased it, if you die it doesn't matter. You don't have the serum in your veins." She pointed out, only to receive a shrug from him.

"I knew that the minute Simmons injected you with the stuff, don't worry about me though. I'm the best since Romanoff remember." He winked which didn't calm her down at all. "I'll get out fine with you by my side. You know I'd never leave you alone." He sighed and held her shoulder in an attempt to comfort her. He pulled her closer and kissed the top of her head. "I promise you won't be leaving without me." He whispered. "But right now, we've just got to brush everything off our shoulders and go back out there okay?" He told her before pressing the button on the tiny machine making the room normal again.

Skye nodded. "So what do I say if someone walks past your bunk as I'm coming out? Won't it look a bit suspicious?" She asked with a smirk, slipping back into her SHIELD persona quickly. "They might think the robot finally confessed his feelings to me and had his way with me." She smirked still and glanced up at him.

Ward just shook his head. "You can be a complete handful at times, you know that?" He laughed and held her a little closer.

"I do." She nodded and kissed his cheek quickly. "I still miss the stubble, Agent Ward." She teased before hitting his shoulder gently and leaving a silent Ward left stood in the middle of his bunk. He ran his hand across his jaw line gently.

He missed the stubble too.

* * *

"An unknown device was used somewhere on the plane."

May stopped punching the bag and turned towards Coulson.

"What are you talking about now?" She sighed and brushed her hair away from her face, still sweaty from her workout. She reached down and grabbed her water.

"I scanned the plane. A device was being used by someone. I talked to FitzSimmons and it was neither of them. I promptly got kicked out before I could ask any more questions because I interrupted their movie night but that's not the point." He rambled slightly. "I'm assuming it wasn't you and I seriously doubt Ward or Skye were behind the use of some kind of crazy device. I have no idea what's going on." He muttered and loosened his tie.

"Why are you ruling the other two out but not FitzSimmons? I get that they work with all sorts of weird things but can't the other two?" She asked with a frown.

"Skye wouldn't, I mean I seriously doubt it. She has her laptop and it wasn't that type of signal and Ward is just.. Ward's just Ward so it's not him." He concluded, not having a better explanation.

May nodded. What he was saying had some truth to it. "Could you not scan where it was coming from?" Coulson shook his head. "So what do you think it is?"

"I have no idea, considering we're a multi-billion dollar company I would have thought we could have better devices for things like this." He sighed, "Do you think maybe I should talk to the other two then? Skye's a bad liar, so it will rule her out. Ward's gonna need a different way of being asked, he's the best since Romanoff and we know she can beat any lie detector." He told her.

"Just go too intense on either of them?" May requested, "There's a chance it's not them and we don't want to mess them about." She warned before turning her head again. "I'm gonna go shower, tell me if you find anything out." She sighed before walking away.

* * *

Ward and Skye had both been called into the main area of the Bus, Skye eating the sandwich she'd taken from Ward when he turned away to face Coulson a few minutes ago. Ward was sat in the single arm chair besides Skye while she took up most of the three seater sofa.

"This will be quick so don't worry about that aspect of things but I just have a few questions to ask you both." He started, as if it was a full on interrogation. "Earlier today I picked up an unknown signal somewhere on the Bus and I just need to check it was neither of you before the Hub finds out because if I don't phone in with a reason to it the report gets sent off, stating there's a dangerous item onboard." He told them and folded his arms.

Ward turned his head to look at Skye. "Have something to admit to this time?" He asked her, much like he had wanted to after the whole Miles 'scandal'. "I'm sure he'd appreciate it much more this time round if you told us all you knew about something." He muttered sarcastically.

"That's not fair." She frowned at him before turning back to Coulson. "I swear it wasn't me." She promised him, it was technically true, it was Ward who pressed the button. "And yes, you can trust me this time." She said before glaring at Ward for a few seconds.

"Well sir, it wasn't me either." Ward replied, looking up at the man who was stood beside him.

Coulson nodded with a sigh. "I was hoping either of you would admit to something, means the chances of us getting called back to the Hub would have been lower." He told them before nodding to himself. "Well thank you both, sorry for interrupting you both."

As Coulson left Skye turned to Ward, who still looked as relaxed as ever, "What do we do?" She hissed and he turned to look at her, the serious look still on his face.

"Just keep in character." He mumbled close to her as he stood up. "That's all we can do, other than hope Garrett can sort something out back at the Hub, if not we know what we need to do." He told her, a conflicted look suddenly appearing on his face, he didn't want to take anyone out but if necessary he would, especially if it meant helping or even saving Skye.

"We can't do that, it's a - " She was cut of by Ward.

"We do what's needed, I won't hesitate, will you?" He asked before turned and left her on her own.

* * *

 **So this was kind of a filler before the main drama kicks in, I'm already writing chapter 3 so hopefully you won't have to wait as long for it to be updated, college and personal things got in the way of posting this so I apologise!** :)


	3. Chapter 3

**Sorry for the reupload by the way, spotted a mistake in my notes just after I posted it.**

 **8abbie8: I've never written FitzSimmons before but I'm planning on adding hints of it here and there eventually, I'm just getting this first bit set up and then hopefully you'll be seeing more of them :D**

 **Thank you to SparkyGirl123 for beta reading this!**

* * *

As they had all expected, they'd been called back to the Hub by Fury's direct orders, obviously he'd wanted to make sure one of his favourite and most valued agents was as safe as possible considering his job. They had all gotten off the Bus, Ward had grabbed a few important things first and hidden them on himself, and grabbed their passes and were free to wander around certain parts of the large Shield base.

As they had only a few months prior, FitzSimmons rushed off towards the labs, most likely to continue analysing Skye's blood while Coulson and May went to go talk to Fury about the mishap on the plane, which left Skye and Ward in each others company.

"We need to go speak to the two scientists." Ward muttered to her and ran his hand through his hair, in frustration. He had hoped they'd be distracted for long enough he could take the samples from them. "They can't find anything out or he'll kill me." He muttered to her, being careful not to use Garrett's name in case other agents overheard him, he couldn't get into trouble, especially here of all places.

"Wait, hang on, you said you wouldn't die." Skye mumbled and turned to look up at him, a frown on her face.

"Well that was before I realised this was going to be harder than I originally thought." He told her before nodding his head in the direction that the two young scientists went in. "C'mon, we'll just have to sweet talk them."

"You don't do sweet talk, you never have." She muttered under her breath as she followed him. She knew it was a mission all along but the thought of killing the people she had grown close to was slowly beginning to feel weird to her, she wasn't too sure about her partner though. He owed more than she did to their actual SO but he couldn't kill their current team, could he?

"You're right, I was just being polite." He told her bluntly, not completely sure if he was meant to hear her. He knew she was turning 'soft' as Garrett would put it and while he wanted her to stay beside his side for as long as possible, she'd be safer in Shield but then there would be the chance he'd be discovered as the worse of the pair. He couldn't have that. Not after they had got this far. "We also need to talk later on, just us two this time." He told her before he walked at a quicker pace ahead of her, fixing his jacket sleeves slightly, Skye now trailing behind slightly, a confused look on her face.

Once in the lab, Ward reached over and turned the computer off that Simmons was working on, much to her outrage. "I'm going to need to take Skye blood work from you." He told her, no emotion showing on his face or in his voice. "Coulson's order." He warned and nodded towards the samples and paperwork that was beside her, Fitz was just watching with a frown.

"What? No..Of course not..Do you not understand what this could do? It could save agent's lives." She said confidently and moved closer to her work so he couldn't take it, even though she knew if he really wanted he could take her out and she wouldn't even be aware of it.

"It could, but we also don't know the other possible side effects of it. Coulson wanted it to stay on the Bus, we're not on the Bus." He explained, it wasn't all lies really, he had ordered that.

"If he wants it he can come and get it."

"I know you're not that stupid Simmons, we're only here because Fury wanted words with him. I can't just ask him to 'pop' over here." He pointed out and stepped closer again.

Simmon's glanced over at Skye who was stood there with a frown on her face, directed at Ward.

"Grant, just leave it for now, we'll get Coulson over afterwards." Skye told him calmly, this caused him to spin around to face her.

"Do you not understand? I'm following an order." He told her, hoping she'd catch on that it was Garrett's order, not Coulson. "I have get the stuff from them, like we were told to do." He explained and made no effort to move closer.

"And this isn't the way to do this, Ward. So stop." She told him as if it were a command.

"You heard him earlier today right? I don't get this stuff you'll most likely be the only one walking away from all this." He snapped before his eyes widened, quickly remembering they weren't the only ones in the room.

"What are you two talking about..?" Fitz asked as he came and stood beside his fellow British scientist. "That doesn't sound very Coulson like." He stated.

"You're right." He muttered and turned to glance at the pair. "So now we're down to this.. Are you going to hand me that?" Ward asked, nodding towards everything as the pair shook their head, without hesitation Ward pulled out his icer and shot the two. He could hear Skye gasping behind him as he stepped over their bodies and grabbed all the stuff he deemed important, he then turned back to Skye who was wearing a concerned expression. "Relax, they'll be fine. Our cover is still intact, one of the Hydra scientists managed to lace it with a hint of the memory loss stuff they found a while back." He told her. "They'll wake up in a few minutes just concerned about everything they lost, which Garrett will have and I will still be breathing." Grant said, the last bit more sarcastically than anything. "You with me?"

Skye just nodded, unable to say anything as she looked down at her friends. "Yeah, sorry.."

"You know I wouldn't have had to do that if they'd cooperated with me right?" He asked and walked the short distance to her until her could place his left hand on her shoulder, his right holding everything they needed. "Now before we go, we need to go find Garrett, are you coming or do you want to wait until they wake up?" He offered, knowing she'd appreciate the gesture.

"I'll make sure no one comes and sees them and then I'll come find you." She smiled and kissed his cheek gently. "Stay safe."

"Of course I will, I have this now don't I?" Grant said with a smirk, "Promise you'll come find me? I don't like the idea of not knowing if you've been hurt or whatever, you know that after that stupid stunt he pulled." He practically growled.

"Just don't bring that up to him and you'll be fine." Skye sighed. "I'll come straight to you." She smiled softly.

"I'll see you later then." He mumbled before walked past her and out the door, just in time for FitzSimmons to come back around.

"Hey, guys." She smiled as she rushed forward to help them sit up.

* * *

 **So another bit of drama added in there, i finally have a plan for the next few chapters so updates should follow soon again!**

 **So 1000 people have read this now which is amazing so thanks to you all!**

 **Also, Brett favourited my tweet yesterday and I'm still freaking out, I was crying it wasn't pretty xD**


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